Even a future Hurricane Sandy can’t sour plans to bring Brooklyn’s biggest waterfront project to the former Domino Sugar plant in Williamsburg.

Two Tree Management Co. says it plans to build four new apartment and office towers for the $1.5 billion project more than 150 feet back from the riverfront.

Under an earlier design by developer CPC Resources — which pulled out of the 11-acre project last year because of money troubles – apartment towers would’ve been built 50 feet from the East River despite being in a storm-unfriendly “Zone A” evacuation area.

“This project will prove that we can continue to do waterfront development in the city and not have to run from the water,” said Vishaan Chakrabarti, a principal at SHoP Architects, which is designing the project for Two Trees’ father-and-son principals, David and Jed Walentas.

Chakrabarti said the redesign raises front-door entrances up another three feet – above new flood plains recently set by the feds following Sandy – by adding some stairs and moving the project more uphill.

Cul-de-sacs once planned between buildings have been removed – not only to improve neighborhood waterfront access, but also to avoid potential flooding from pooling water runoff during storms. The sloping streets would instead allow storm water to flow into the river.

The project’s open space has been expanded by 60 percent to 5.3 acres. Chakrabarti said the new parkland will use little pavement and “act as a sponge” for heavy rains.

Other storm-friendly new features include moving the heating, ventilation and power systems out of the basement. They will be placed at least two-stories above ground and out of danger from Mother Nature.

Jed Walentas said Two Trees – best known for its projects in Dumbo — remains “100 percent committed to waterfront development post-Sandy.”

“Our vision for the Domino site shows that with smart planning we can make it work and keep it safe,” he added.

Domino’s landmarked refinery building – which will be converted into office space for the development – is already located out of the flood plain.